Sound Editing Tools
Audacity (for all platforms, Highly Recommended***)
Goldwave (for Windows)
Spark ME (for MAC)
Cacophony (for MAC)
Audiocorder (for MAC)
AudioXplorer (for MAC)
Soundhack (for MAC)
Ardour
Sweep (for Linux)

Pure Data
download pd-extended .37 here: pd (for all platforms)
other pd resources: Miller Puckette Home | Pure Data External Repository | Pure Data Archive | Percolate | Pure Data Base

Cycling '74 Products
Max/MSP/Jitter etc (you have to buy these)

SSUM
Signals and Systems using MATLAB

MARSYAS
marsyas

Music Notation Programs
Harmony Assistant X (for MAC)
NoteAbility Pro (for MAC)